NSF-BSF: Synchronous electro-optical DNA detection using low-noise dielectric nanopores on sapphire

纳米孔DNA传感是一项新兴的技术，近年来已经发展到检测DNA初级序列和表观遗传信息（如甲基化），这对基础生物学和精密医学都至关重要。然而，在纳米孔中高速准确的DNA甲基化检测仍然滞后。这是由于导电硅（Si）固有的大电容噪声以及复杂的DNA与纳米孔表面的动态相互作用导致的信噪比（SNR）不足。本项目提出了一个多学科的研究计划，以解决固态纳米孔器件中高速低噪声生物分子传感的基本挑战。新设计在单个传感器平台上结合了电气和光学传感，以提高传感精度。它采用晶体蓝宝石作为绝缘衬底，集成大带隙氧化钛薄膜作为传感元件，以最大限度地减少电子和光学噪声。DNA甲基化检测的演示将证明我们的TiO2/蓝宝石纳米孔传感器在检测复杂分子结构方面的可行性，这将对分子标记检测和分子-分子相互作用产生广泛的影响。教育目标是促进电子纳米传感器相关工程教育的本科生和研究生，并更好地准备他们作为未来的创新者转化纳米生物技术。外联目标是提高公众对纳米传感器在医疗保健中的重要性的认识，并吸引K-12学生和代表性不足的个人参与STEM职业。本研究旨在通过创建一个显著改进的纳米孔传感器平台来填补纳米孔传感研究的知识空白，该平台将低光学背景氧化钛膜集成在低电容和低电噪声的蓝宝石上。研究团队将在蓝宝石上制备小而薄的TiO2膜，建立膜形成和纳米孔钻探的高通量制造方法，进行单分子DNA易位，研究DNA-纳米孔相互作用，并分析甲基化检测数据。提出的传感器平台具有许多关键功能，以支持各种新兴生物分子诊断技术的发展。首先，在绝缘蓝宝石上创建超小型（10 μm）介质膜消除了衬底电导，并且即使对于高介电常数和超薄（5 nm） TiO2器件，也将芯片电容大幅降低到几picofarad，从而显着降低了背景高频电噪声并显着改善了高带宽传感。此外，薄膜的形成和纳米孔的钻孔都将通过高通量制造方法来实现，即晶圆规模和批量加工兼容的蓝宝石蚀刻和直接激光钻孔，从而实现低成本和可重复生产。这种可规模化制造、低噪音、高灵敏度的纳米孔将有助于在单次测量中实现高分辨率基因鉴定和甲基化状态的定量，并大大降低成本。该奖项反映了美国国家科学基金会的法定使命，并通过使用基金会的知识价值和更广泛的影响审查标准进行评估，被认为值得支持。

Nanopore DNA sensing is an emerging technology, and has recently been developed to detect both the DNA primary sequence and epi-genetic information (such as methylation), which is crucial to both fundamental biology and precision medicine.. However, high-speed and accurate DNA methylation detection in nanopores still lags behind. This is attributed to an insufficient signal-to-noise ratio (SNR) resulting from the inherent large electrical capacitive noise from the conductive silicon (Si) and also the complex DNA dynamic interaction with nanopore surface. This project proposes a multidisciplinary research plan to address the fundamental challenges in high-speed and low-noise biomolecular sensing in a solid-state nanopore device. The new design combines electrical and optical sensing on a single sensor platform to improve the sensing accuracy. It utilizes crystalline sapphire as an insulating substrate and integrates large-bandgap titanium oxide thin film as the sensing element to minimize both the electronic and optical noise. The demonstration of DNA methylation detection will prove the feasibility of our TiO2/sapphire nanopore sensors in detecting complex molecular structures that will have broad impact on molecular marker detection and molecule-molecule interactions. The educational objectives are to promote electronic nanosensors related engineering education to undergraduate and graduate students, and to better prepare them as future innovators to transform nanobiotechnologies. The outreach objectives are to promote public awareness of the importance of nanosensors in health care and to attract the participation of K-12 students and underrepresented individuals in STEM careers.This research is to fill the knowledge gap in nanopore sensing research by creating a significantly improved nanopore sensor platform that integrates low-optical background titanium oxide membranes on low-capacitance and hence low-electrical-noise sapphire. The research team will fabricate small and thin TiO2 membranes on sapphire, establish high-throughput manufacturing methods for both membrane formation and nanopore drilling, perform single-molecule DNA translocation, study the DNA-nanopore interaction, and analyze the data for methylation detection. The proposed sensor platform has a number of key features to support the development of a wide variety of emerging biomolecular diagnostic technologies. First, the creation of ultrasmall (10 μm) dielectric membranes on insulating sapphire eliminates substrate conductance, and drastically minimizes the chip capacitance to a few picoFarads even for high-dielectric-constant and ultrathin (5 nm) TiO2 devices, thus significantly reducing the background high-frequency electrical noise and markedly improving high-bandwidth sensing. Further, both membrane formation and nanopore drilling will be achieved by high-throughput manufacturing methods, i.e. wafer-scale and batch-processing compatible sapphire etching and direct laser drilling, thus enabling low-cost and repeatable production. The scalably manufactured, low-noise, high-sensitivity nanopores will facilitate high-resolution gene identification and quantitation of their methylation status in a single measurement and at a greatly reduced cost.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.